extract_clinvar: Extract the genes and variants related to a genetic disorder...

In VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature

Description

extract_clinvar extracts the genes and variants associated to a known genetic disorder or a clinical feature from NCBI ClinVar database. It annotates the phenotypes from GeneReview, MedGen, and OMIM. The alias of a disease/phenotye are considered in HPO database. Furtherly, the variants on a use-defined gene list can be captured at the same time.

Usage

extract_clinvar(keyword, localPDB.path = paste(getwd(),"localPDB",sep="/"), 
           type = "both", HPO.disease = NULL, genelist = NULL, OMIM = NULL)

Arguments

keyword	character string: keyword, to describe a disease, clinical feature, or phenotype.
localPDB.path	the path of localized public data bases. The default value is set in the working directory.
type	the type of the information to extract, must be one of "gene", "variant", "both"(default).
HPO.disease	MIM number of the disease. The default value is NULL, which means that all the MIM number of the disease in HPO are added.
genelist	the gene(s) associated to the disease, or the genes you are interested.
OMIM	whether use the information from OMIM database. The default value is NULL. It can be set 'yes' when you make sue you have a OMIM API key.

Details

The function extracts the genes and variants associated to a disease, clinical feature or phenotype from ClinVar database. The keyword is searched not only in ClinVar, but also in HPO to considered the different alias of a diesease. You can prepare the files from OMIM, ClinVar, Orhanet, Uniprot, HPO, MedGen, and GeneReview using localPDB() before you start the job, which maybe more efficient. More details ablout ClinVar can be seen from http://www.ncbi.nlm.nih.gov/clinvar/.

Value

A list containing two components:

gene2dis	subset of the file gene_condition_source_id, which include all the information about genes and phenotypes in ClinVar.
variants	subset of the file variant_summary.txt, but added sevetal colomns which describe the phenotype from GeneReview, MedGen, and OMIM databases.

Author(s)

Zongfu Cao ([e-mail])

References

1.Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan 1;42(1):D980-5. doi: 10.1093/nar/gkt1113. PubMed PMID: 24234437

2.Melissa Landrum, PhD, Jennifer Lee, PhD, George Riley, PhD, Wonhee Jang, PhD, Wendy Rubinstein, MD, PhD, Deanna Church, PhD, and Donna Maglott, PhD. ClinVar. http://www.ncbi.nlm.nih.gov/books/NBK174587/

3.Sebastian K?hler, Sandra C Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi:10.1093/nar/gkt1026

See Also

pheno_extract_HPO, extract_omim, extract_uniprot, extract_genes_orphanet

Examples

#    library(VarfromPDB)
#    clinvar.phenotype = extract_clinvar(keyword="retinoblastoma")
#    genes.clinvar = clinvar.phenotype[[1]]
#    print(dim(genes.clinvar))
#    variants.clinvar = clinvar.phenotype[[2]]
#    print(dim(variants.clinvar))

Example output

Loading required package: XML
Loading required package: XML2R
Loading required package: curl
Loading required package: stringr

VarfromPDB documentation built on May 2, 2019, 2:10 a.m.